Mineralization of microbial biomass is a common phenomenon in geothermal habitats, but knowledge of the structure of the minerals formed in these environments is limited. A combination of spectroscopic, microscopic, and stable isotopic methods, as well as the chemical analysis of spring water, were employed in the present study to characterize calcium carbonate minerals deposited in filamentous cyanobacterial mats in different locations of La Duke hot spring, a circumneutral thermal feature near the north entrance of Yellowstone National Park, Montana, USA. Calcite was the primary crystalline mineral phase associated with biofilm-containing deposits closest to the source of the spring and the suspended microbial biomass in a pool further from the source. The carbonate minerals at all sites occurred as aggregated granules, ~2 μm in diameter, in close association with the microbial biomass. Only in the deposits closest to the source were the granules organized as laminated structures interspersed with microbial biomass. The calcium carbonate grains contained two distinct regions: a dense monolithic calcite core and a porous dendritic periphery containing organic matter (OM). Electron energy loss spectroscopy (EELS) indicated that the voids were infilled with OM and carbonates. The EELS technique was employed to distinguish the source of carbon in the organic matter and carbonate mixture. The studies of carbon isotope compositions of the calcium carbonates and the saturation indices for calcite in the spring waters suggest that processes (abiotic vs. biotic) controlling the carbonate formation may vary among the sampling sites.

Secondary electron (SE) doping contrast in the scanning electron microscope is correlated with Fermi level pinned surfaces of Si samples prepared using HF-based wet-chemical treatment or focused ion beam (FIB) micromachining en route to quantitative dopant profiling. Using energy-resolved SE imaging techniques and finite-element analyses of surface states and surface junction potentials, we clarified the surface band-bending effects post-NH4F-treatment, consistent with brighter p-contrast from degenerately doped (>1019 cm−3) regions. In general, SE spectromicroscopy scan measurements unambiguously indicated heavy suppression of patch fields, while the empirical discovery of scan frequency-modulated contrast inversion due to Chee et al. [Springer Proceedings in Physics, 120, pp. 407–410 (2008)] is ascribable to competing fixed oxide charge and dynamic charge injection phenomena (particularly at dwell times >29 μs). Leveraging numerical simulations of electric potentials and variable-voltage experimental data, the theoretical model based on amorphization damage-mediated Fermi level pinning is elucidated for Ga+ FIB-processed site-specific doping contrast on patch field-free surfaces. This work successfully argues against the notion that doping contrast ultimately or exclusively entails patch fields or adventitious metal–semiconductor contacts.

Cryo-electron tomography (cryo-ET) is a powerful technique that can provide unprecedented insight into protein-protein interactions and molecular machinery in a near-native state. The adoption of cryo-ET by life science research groups is hampered by the challenges associated with cryo-ET sample preparation. The current sample preparation process has many steps at which ice contamination may occur to negatively affect the final sample and data quality. A survey was conducted to better understand the effects and impact of ice contamination to the cryo-ET outcome. Over 80 cryo-electron microscopy users worldwide participated in our survey. The results are presented in this article. We furthermore discussed the currently available solutions that can alleviate the ice contamination problems to increase the sample yield and cryo-ET data output.

A focused ion beam (FIB) technique describing the preparation of specimens for in situ thermal and electrical transmission electron microscopy is presented in detail. The method can be applied to a wide range of materials and allows the sample to be thinned down to electron transparency while it is attached to the in situ chip. This offers the advantage that the specimen can have a quality in terms of contamination and damage due to the ion beam that is comparable to samples prepared by means of conventional FIB preparation. Additionally, our technique can be performed by most commercially available FIB devices and only requires three simple, custom stubs for the procedure. This should enable a large userbase for this type of sample fabrication. One further benefit of our technique is that the in situ chip can be reused to create another sample on the same chip. The quality of the samples is demonstrated by high-resolution transmission electron microscopy as well as electron energy loss spectroscopy.

Based on technologies capable of data collection between the millimeter and nanometer scales, correlative imaging has been transforming how researchers obtain molecular and spatial information from specimens. Attempts to combine multidimensional data are often met with the challenge of overcoming suboptimal sample conditions such as reduced fluorescence signal, poor specimen preservation, anisotropic specimen deformation, and low specimen contrast. These issues motivated the development and use of enhanced sample preparation procedures, as well as specialized imaging software to overcome such challenges. In this work we present three simple methods to correlate optical and scanning electron microscopy images.

Tomography using a focused ion beam (FIB) combined with a scanning electron microscope (SEM) is well-established for a wide range of conducting materials. However, performing FIB–SEM tomography on ion- and electron-beam-sensitive materials as well as poorly conducting soft materials remains challenging. Some common challenges include cross-sectioning artifacts, shadowing effects, and charging. Fully dense materials provide a planar cross section, whereas pores also expose subsurface areas of the planar cross-section surface. The image intensity of the subsurface areas gives rise to overlap between the grayscale intensity levels of the solid and pore areas, which complicates image processing and segmentation for three-dimensional (3D) reconstruction. To avoid the introduction of artifacts, the goal is to examine porous and poorly conducting soft materials as close as possible to their original state. This work presents a protocol for the optimization of FIB–SEM tomography parameters for porous and poorly conducting soft materials. The protocol reduces cross-sectioning artifacts, charging, and eliminates shadowing effects. In addition, it handles the subsurface and grayscale intensity overlap problems in image segmentation. The protocol was evaluated on porous polymer films which have both poor conductivity and pores. 3D reconstructions, with automated data segmentation, from three films with different porosities were successfully obtained.

A new transmission electron microscopy (TEM) specimen preparation method that utilizes a combination of focused ion beam (FIB) methods and ultramicrotomy is demonstrated. This combined method retains the benefit of site-specific sampling by FIB but eliminates ion beam-induced damage except at specimen edges and allows recovery of many consecutive sections. It is best applied to porous and/or fine-grained materials that are amenable to ultramicrotomy but are located in bulk samples that are not. The method is ideal for unique samples from which every specimen is precious, and we demonstrate its utility on fine-grained material from the one-of-a-kind Paris meteorite. Compared with a specimen prepared by conventional FIB methods, the final sections are uniformly thin and free from re-deposition and curtaining artifacts common in FIB specimens prepared from porous, heterogeneous samples.

It is shown that a xenon plasma focused ion beam (FIB) microscope is an excellent tool for high-quality preparation of functional oxide thin films for atomic resolution electron microscopy. Samples may be prepared rapidly, at least as fast as those prepared using conventional gallium FIB. Moreover, the surface quality after 2 kV final polishing with the Xe beam is exceptional with only about 3 nm of amorphized surface present. The sample quality was of a suitably high quality to allow atomic resolution high-angle annular dark field imaging and integrated differential phase contrast without any further preparation, and the resulting images were good enough for quantitative evaluation of atomic positions to reveal the oxygen octahedral tilt pattern. This suggests that such xenon plasma FIB instruments may find widespread application in transmission electron microscope and scanning transmission electron microscope specimen preparation.

High-resolution imaging of electron-transparent samples using a scanning electron microscope, here termed low voltage (LV) STEM, is a new and valuable technique for studying Earth and planetary materials. The most effective method of LV-STEM imaging uses a pair of electron detectors positioned side-by-side beneath the thin sample. The detector directly underlying the sample forms bright-field images dominated by mass-thickness contrast. Activation of the detector offset from the sample yields dark-field images with a greater component of atomic number contrast. LV-STEM images with significant diffraction contrast can also be obtained, but require careful positioning of the sample relative to the electron detectors. In this study LV-STEM was used successfully to image sub-μm sized kaolinite crystals and tens of nm-sized etch pits on the gold-coated surfaces of weathered feldspar grains. Dark-field LV-STEM was also especially effective for characterizing very fine-scale intergrowths of Mg- and Fe-rich phyllosilicates within uniformly thin samples of the Murchison meteorite prepared using the focused ion beam (FIB) technique. LV-STEM is a quick and easy method for characterizing the morphology and internal structure of mineral and rock samples and may prove to be especially useful in geomicrobiology research.

Using high intensity beams of fast electrons, the transmission electron microscope (TEM) and scanning transmission electron microscope (STEM) enable comprehensive characterization of rocks and minerals at micrometre to sub-nanometre scales. This review outlines the ways in which samples of Earth and planetary materials can be rendered sufficiently thin for TEM and STEM work, and highlights the significant advances in site-specific preparation enabled by the focused ion beam (FIB) technique. Descriptions of the various modes of TEM and STEM imaging, electron diffraction and X-ray and electron spectroscopy are outlined, with an emphasis on new technologies that are of particular relevance to geoscientists. These include atomic-resolution Z-contrast imaging by high-angle annular dark-field STEM, electron crystallography by precession electron diffraction, spectrum mapping using X-rays and electrons, chemical imaging by energy-filtered TEM and true atomic-resolution imaging with the new generation of aberration-corrected microscopes. Despite the sophistication of modern instruments, the spatial resolution of imaging, diffraction and X-ray and electron spectroscopy work on many natural materials is likely to remain limited by structural and chemical damage to the thin samples during TEM and STEM.

Transmission electron microscope samples were prepared of ALH 78045 and ALH 88045, two clay-and phyllosilicate-bearing Antarctic meteorites, using argon ion milling and focused ion beam (FIB) techniques. ALH 78045 contains clay- and phyllosilicate-filled veins that have formed by terrestrial weathering of olivine, orthopyroxene and metal. Very narrow (∼10 nm) intragranular clay-filled veins could be observed in the TEM samples prepared by argon ion milling, whereas differential thinning and lack of precision in the location of the electron-transparent areas hindered the study of wider (5 — 15 μm) phyllosilicate-filled intergranular veins. Using the FIB instrument, electron-transparent slices were cut from specific parts of the wider veins and lifted out for TEM study. Results show that these veins are occluded by cronstedtite, a mixed-valence Fe-rich phyllosilicate. This discovery shows that silicates can be both dissolved and precipitated during terrestrial weathering within the Antarctic ice. ALH 88045 is one of a small number of known CM1 carbonaceous chondrites. This meteorite is largely composed of flattened ellipsoidal aggregates of serpentine-group phyllosilicates. To determine the mineralogy and texture of phyllosilicates within specific aggregates, TEM samples were prepared by trenching into the cut edge of a sample using the FIB instrument. Results show that Mg-rich aggregates are composed of lath-shaped serpentine crystals with a ∼0.73 nm basal spacing, which is typical of the products of low temperature aqueous alteration within asteroidal parent bodies. Results of this work demonstrate that the FIB has enormous potential in a number of areas of Earth and planetary science.

This paper reports on the substantial improvement of specimen quality by use of a low voltage (0.05 to ~1 keV), small diameter (~1 μm), argon ion beam following initial preparation using conventional broad-beam ion milling or focused ion beam. The specimens show significant reductions in the amorphous layer thickness and implanted artifacts. The targeted ion milling controls the specimen thickness according to the needs of advanced aberration-corrected and/or analytical transmission electron microscopy applications.

This letter describes an innovative spin-coating system, built from off-the-shelf components, that can easily and inexpensively be integrated into any laboratory environment. Combined with a liquid suspension of conductive polymer, such a “rotary coater” enables simple coating of planar samples to create a physical protective barrier on the sample surface. This barrier aids in charge dissipation during scanning electron microscope and focused ion beam (FIB) imaging and provides wide-scale protection of the sample surface from ion bombardment during FIB imaging and gas-assisted deposition. This polymer layer replaces the localized and time-consuming electron beam deposition step typically performed during transmission electron microscopy lamella preparation. After observation, the coating can be easily removed, if desired. The described spin-coating procedure has minimal cost while providing repeatable positive results, without the need for expensive commercial coating instrumentation.

Approximately 30 years after the first use of focused ion beam (FIB) instruments to prepare atom probe tomography specimens, this technique has grown to be used by hundreds of researchers around the world. This past decade has seen tremendous advances in atom probe applications, enabled by the continued development of FIB-based specimen preparation methodologies. In this work, we provide a short review of the origin of the FIB method and the standard methods used today for lift-out and sharpening, using the annular milling method as applied to atom probe tomography specimens. Key steps for enabling correlative analysis with transmission electron-beam backscatter diffraction, transmission electron microscopy, and atom probe tomography are presented, and strategies for preparing specimens for modern microelectronic device structures are reviewed and discussed in detail. Examples are used for discussion of the steps for each of these methods. We conclude with examples of the challenges presented by complex topologies such as nanowires, nanoparticles, and organic materials.

The fracture toughness of NiAl single crystals is evaluated with a new method based on the J-integral concept. The new technique allows the measurement of continuous crack resistance curves at the microscale by continuously recording the stiffness of the microcantilevers with a nanoindenter. The experimental procedure allows the determination of the fracture toughness directly at the onset of stable crack growth. Experiments were performed on notched microcantilevers which were prepared by focused ion beam milling from NiAl single crystals. Stoichiometric NiAl crystals and NiAl crystals containing 0.14 wt% Fe were investigated in the so-called “hard” orientation. The fracture toughness was evaluated to be 6.4 ± 0.5 MPa m1/2 for the stoichiometric sample and 7.1 ± 0.5 MPa m1/2 for the iron containing sample, indicating that the addition of iron enhances the ductility. This effect is intensified with ongoing crack propagation where the Fe-containing sample exhibits a stronger crack resistance behavior than the stoichiometric NiAl single crystal. These findings are in good agreement with macroscopic fracture toughness measurements, and validate the new micromechanical testing approach.

The damage and ion distribution induced in Si by an inductively coupled plasma Xe focused ion beam was investigated by atom probe tomography. By using predefined patterns it was possible to prepare the atom probe tips with a sub 50 nm end radius in the ion beam microscope. The atom probe reconstruction shows good agreement with simulated implantation profiles and interplanar distances extracted from spatial distribution maps. The elemental profiles of O and C indicate co-implantation during the milling process. The presence of small disc-shaped Xe clusters are also found in the three-dimensional reconstruction. These are attributed to the presence of Xe nanocrystals or bubbles that open during the evaporation process. The expected accumulated dose points to a loss of >95% of the Xe during analysis, which escapes undetected.

Irradiation damage, caused by the use of beams in electron and ion microscopes, leads to undesired physical/chemical material property changes or uncontrollable modification of structures. Particularly, soft matter such as polymers or biological materials is highly susceptible and very much prone to react on electron/ion beam irradiation. Nevertheless, it is possible to turn degradation-dependent physical/chemical changes from negative to positive use when materials are intentionally exposed to beams. Especially, controllable surface modification allows tuning of surface properties for targeted purposes and thus provides the use of ultimate materials and their systems at the micro/nanoscale for creating functional surfaces. In this work, XeF2 and I2 gases were used in the focused ion beam scanning electron microscope instrument in combination with gallium ion etching of high-density polyethylene surfaces with different beam currents and accordingly different gas exposure times resulting at the same ion dose to optimize and develop new polymer surface properties and to create functional polymer surfaces. Alterations in the surface morphologies and surface chemistry due to gas-assisted etching-based nanostructuring with various processing parameters were tracked using high-resolution SEM imaging, complementary energy-dispersive spectroscopic analyses, and atomic force microscopic investigations.

We investigated the effect of focused ion beam (FIB) imaging on the crystallinity of InAs using Raman scattering. A spatial correlation model was used to fit the broad band induced by FIB imaging. The fitting gives a correlation length of ~42 Å for the noisiest image condition (with an ion fluence of 7.4×1010 cm−2), implying severe damage in the surface layer of InAs. However, further increasing the fluence by several orders of magnitude only decreases the correlation length from 42 to 35 Å. We attribute the severe damage to the high beam current density and the low scanning speed of the FIB imaging process. These process conditions, along with low InAs thermal conductivity, also leads to a high local temperature in the exposed region that largely annihilated the defects and resulted in the nearly fluence-independent behavior.

Various practical issues affecting atom probe tomography (APT) analysis of III-nitride semiconductors have been studied as part of an investigation using a c-plane InAlN/GaN heterostructure. Specimen preparation was undertaken using a focused ion beam microscope with a mono-isotopic Ga source. This enabled the unambiguous observation of implantation damage induced by sample preparation. In the reconstructed InAlN layer Ga implantation was demonstrated for the standard “clean-up” voltage (5 kV), but this was significantly reduced by using a lower voltage (e.g., 1 kV). The characteristics of APT data from the desorption maps to the mass spectra and measured chemical compositions were examined within the GaN buffer layer underlying the InAlN layer in both pulsed laser and pulsed voltage modes. The measured Ga content increased monotonically with increasing laser pulse energy and voltage pulse fraction within the examined ranges. The best results were obtained at very low laser energy, with the Ga content close to the expected stoichiometric value for GaN and the associated desorption map showing a clear crystallographic pole structure.

The dehydrogenated microstructure of the lithium borohydride-yttrium hydride (LiBH4-YH3) composite obtained at 350°C under 0.3 MPa of hydrogen and static vacuum was investigated by transmission electron microscopy combined with a focused ion beam technique. The dehydrogenation reaction between LiBH4 and YH3 into LiH and YB4 takes place under 0.3 MPa of hydrogen, which produces YB4 nano-crystallites that are uniformly distributed in the LiH matrix. This microstructural feature seems to be beneficial for rehydrogenation of the dehydrogenation products. On the other hand, the dehydrogenation process is incomplete under static vacuum, leading to the unreacted microstructure, where YH3 and YH2 crystallites are embedded in LiBH4 matrix. High resolution imaging confirmed the presence of crystalline B resulting from the self-decomposition of LiBH4. However, Li2B12H12, which is assumed to be present in the LiBH4 matrix, was not clearly observed.